8DZK

Dbr1 in complex with 5-mer cleavage product

8DZK の概要

• エントリーDOI: 10.2210/pdb8dzk/pdb
• 分子名称: RNA lariat debranching enzyme, putative, RNA (5'-R(P*(G46)P*UP*GP*UP*U)-3'), FE (II) ION, ... (6 entities in total)
• 機能のキーワード: metalloenzyme, complex, branched rna, hydrolase-rna complex, rna binding protein, hydrolase/rna
• 由来する生物種: Entamoeba histolytica; 詳細
• タンパク質・核酸の鎖数: 10
• 化学式量合計: 215245.13

構造登録者

Clark, N.E.,Taylor, A.B. (登録日: 2022-08-08, 公開日: 2022-08-24, 最終更新日: 2023-10-25)

主引用文献

Clark, N.E.,Katolik, A.,Welch, A.,Schorl, C.,Holloway, S.P.,Schuermann, J.P.,Hart, P.J.,Taylor, A.B.,Damha, M.J.,Fairbrother, W.G.
Crystal Structure of the RNA Lariat Debranching Enzyme Dbr1 with Hydrolyzed Phosphorothioate RNA Product.
Biochemistry, 61:2933-2939, 2022

PubMed Abstract: The RNA lariat debranching enzyme is the sole enzyme responsible for hydrolyzing the 2'-5' phosphodiester bond in RNA lariats produced by the spliceosome. Here, we test the ability of Dbr1 to hydrolyze branched RNAs (bRNAs) that contain a 2'-5'-phosphorothioate linkage, a modification commonly used to resist degradation. We attempted to cocrystallize a phosphorothioate-branched RNA (PS-bRNA) with wild-type Dbr1 (EhDbr1) but observed in-crystal hydrolysis of the phosphorothioate bond. The crystal structure revealed EhDbr1 in a product-bound state, with the hydrolyzed 2'-5' fragment of the PS-bRNA mimicking the binding mode of the native bRNA substrate. These findings suggest that product inhibition may contribute to the kinetic mechanism of Dbr1. We show that Dbr1 enzymes cleave phosphorothioate linkages at rates ∼10,000-fold more slowly than native phosphate linkages. This new product-bound crystal structure offers atomic details, which can aid inhibitor design. Dbr1 inhibitors could be therapeutic or investigative compounds for human diseases such as human immunodeficiency virus (HIV), amyotrophic lateral sclerosis (ALS), cancer, and viral encephalitis.

PubMed: 36484984
DOI: 10.1021/acs.biochem.2c00590

実験手法

X-RAY DIFFRACTION (2.1 Å)